From c1d97724bed6278279b7a0433e38db61e1eda783 Mon Sep 17 00:00:00 2001
From: Sebastian Funk <sebastian.funk@lshtm.ac.uk>
Date: Fri, 22 Sep 2023 19:37:07 +0100
Subject: [PATCH] fix bounds of initial conditions for delays

---
 R/create.R | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/R/create.R b/R/create.R
index 0e5098b74..65614c2d4 100644
--- a/R/create.R
+++ b/R/create.R
@@ -513,8 +513,12 @@ create_initial_conditions <- function(data) {
   init_fun <- function() {
     out <- list()
     if (data$delay_n_p > 0) {
+      out$delay_mean <- array(rep(0, data$delay_n_p))
+      lower_bounds <- rep(-Inf, data$delay_n_p)
+      ## gamma
+      lower_bounds[data$dist == 1] <- 0
       out$delay_mean <- array(truncnorm::rtruncnorm(
-        n = data$delay_n_p, a = 0,
+        n = data$delay_n_p, a = lower_bounds,
         mean = data$delay_mean_mean, sd = data$delay_mean_sd * 0.1
       ))
       out$delay_sd <- array(truncnorm::rtruncnorm(